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Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.
Code accompanied to the SharePro for colocalization analysis paper
A powerful TWAS framework leveraging summary-level reference data
Repo for mRNA and protein expression QTLs (e/pQTLs) analysis utilizing the Japan COVID-19 Task Force dataset
Cellular dynamics across aged human brains uncover a multicellular cascade leading to Alzheimer’s disease
Analysis of gene expression and splicing diversity in a subset of samples from the 1000 Genomes Project, including eQTL and sQTL discovery and annotation.
Analyzing and visualizing KEGG information using the grammar of graphics
Data analysis for Stankey CT et al, 2024.
This study benchamrked the performance of existing cell deconvolution methods with human brain transcriptome and evaluated the biological applications of deconvoluted data in eQTL mapping and diffe…
MultiSuSiE is a multi-ancestry extension of the Sum of Single Effects model
Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper
A curated and summarized list of bioinformatics bench-marking papers and resources.
A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
Cell-type-specific Alzheimer's disease polygenic risk score
A package to estimate biological organ age using SomaScan plasma proteomics data
Introduction to Computational Biology and Bioinformatics Course at Caltech, 2023
Plugins for the Ensembl Variant Effect Predictor (VEP)
An accurate and efficient colocalization method accounting for multiple causal signals
Gene group activity utility functions for Scanpy
Perform differential expression analysis on cohort-scale single cell datasets using linear mixed models
gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
R package for querying the DrugBank database in batch locally